def test_set_update(self):
trial = set_updated(self.trial)
assert 'last_updated' in trial, trial
trial = self._check_trial_post(trial)
# send again
trial = set_updated(trial)
assert 'last_updated' in trial, trial
assert 'curated_on' in trial and trial['curated_on'] == '', trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n %s' % (trial['_summary'], field)
self._check_trial_post(trial)
# curate
trial = set_curated(trial)
assert 'last_updated' in trial, trial
assert 'curated_on' in trial and trial['curated_on'], trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'], field)
self._check_trial_post(trial)
def test_set_update(self):
trial = set_updated(self.trial)
trial = self._prep_trial(trial)
assert 'last_updated' in trial, trial
build_trial_elasticsearch_fields([trial])
# send again
trial = set_updated(trial)
build_trial_elasticsearch_fields([trial])
assert 'last_updated' in trial, trial
assert 'curated_on' in trial and trial['curated_on'] == '', trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n %s' % (
trial['_summary'], field)
# curate
trial = set_curated(trial)
assert 'last_updated' in trial, trial
assert 'curated_on' in trial and trial['curated_on'], trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'],
field)
def test_set_update(self):
trial = set_updated(self.trial)
assert 'last_updated' in trial, trial
trial = self._check_trial_post(trial)
# send again
trial = set_updated(trial)
assert 'last_updated' in trial, trial
assert 'curated_on' in trial and trial['curated_on'] == '', trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n %s' % (
trial['_summary'], field)
self._check_trial_post(trial)
# curate
trial = set_curated(trial)
assert 'last_updated' in trial, trial
assert 'curated_on' in trial and trial['curated_on'], trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'],
field)
self._check_trial_post(trial)
def test_updatedt_with_curatedt(self):
# set up
today = dt.datetime.now().strftime('%B %d, %Y')
old = 'October 27, 2016'
on_trial['_genomic'] = {'hugo_symbol': [{'value': 'TEST'}]}
on_trial['_clinical'] = {'disease_status': [{'value': ['TEST']}]}
# set both dates to OLD
on_trial['curated_on'] = old
on_trial['last_updated'] = old
assert on_trial['curated_on'] == old, self._debug(
on_trial, 'curated_on')
assert on_trial['last_updated'] == old, self._debug(
on_trial, 'last_updated')
# set "last_updated" to TODAY
trial = set_updated(on_trial)
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(
trial, 'last_updated')
# check dates are preserved after trial_insert is called
trial['protocol_no'] = '01-001'
trial = trial_insert([trial])
trial = trial[0]
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(
trial, 'last_updated')
# check the other way around
on_trial['curated_on'] = old
trial['last_updated'] = old
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == old, self._debug(trial, 'last_updated')
trial = set_curated(on_trial)
assert trial['curated_on'] == today, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(
trial, 'last_updated')
trial = trial_insert([trial])
trial = trial[0]
assert trial['curated_on'] == today, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(
trial, 'last_updated')
def test_updatedt_with_curatedt(self):
# set up
today = dt.datetime.now().strftime('%B %d, %Y')
old = 'October 27, 2016'
on_trial['_genomic'] = {'hugo_symbol': [{'value': 'TEST'}]}
on_trial['_clinical'] = {'disease_status': [{'value': ['TEST']}]}
# set both dates to OLD
on_trial['curated_on'] = old
on_trial['last_updated'] = old
assert on_trial['curated_on'] == old, self._debug(on_trial, 'curated_on')
assert on_trial['last_updated'] == old, self._debug(on_trial, 'last_updated')
# set "last_updated" to TODAY
trial = set_updated(on_trial)
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(trial, 'last_updated')
# check dates are preserved after trial_insert is called
trial = trial_insert([trial])
trial = trial[0]
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(trial, 'last_updated')
# check the other way around
on_trial['curated_on'] = old
trial['last_updated'] = old
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == old, self._debug(trial, 'last_updated')
trial = set_curated(on_trial)
assert trial['curated_on'] == today, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(trial, 'last_updated')
trial = trial_insert([trial])
trial = trial[0]
assert trial['curated_on'] == today, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(trial, 'last_updated')
def update_from_oncore(protocol_no):
"""
This processes updates sent directly from oncore. The premise is that a seperate service will
be polling the OnCore database and passing along the JSON formatted trials to here. This service will
need to find the equivalent trial (if a new trial is POSTed here it should be ignored) and compute the update
loging. The logic is divided into two parts:
1. any non-curated field should be updated in MM seamlessly (such as trial and arm status)
2. any curated field (such as match) should not be touched, and a change here should notify the curator
via the email functionality.
"""
db = get_db()
# get the trial.
on_trial = request.get_json(silent=True)
# assert we have an existing one.
mm_trial = db['trial'].find_one({"protocol_no": protocol_no})
if mm_trial is None:
logging.warning("oncore posted trial that is not in database: %s" %
protocol_no)
return json.dumps({"success": True})
# USED TO GENERATE TESTING FILES.
#with open("tests/data/oncore/%s.json" % protocol_no, "w") as fout:
# json.dump(oncore_trial, fout)
# save relavent information for update.
trial_id = str(mm_trial['_id'])
etag = mm_trial['_etag']
# call the comparison.
cmp = OncoreSync()
mm_trial, updated, changes = cmp.compare_trials(on_trial, mm_trial)
for log_entry in cmp.log_entries:
db.oncore_trial_log.insert(log_entry)
post_mattermost(msg='Trial Update', hashtag='#OnCore', data=log_entry)
cmp.send_email()
# if it is updated then do the update.
if updated:
# strip meta
for key in list(mm_trial.keys()):
if key[0] == "_":
del mm_trial[key]
mm_trial['_id'] = trial_id
# set headers.
headers = {
'Content-Type':
'application/json',
'Authorization':
'Basic ' +
base64.b64encode(f'{API_TOKEN}:'.encode('utf-8')).decode('utf-8'),
'If-Match':
etag
}
# set last updated field
mm_trial = set_updated(mm_trial)
# post the trial.
url = '%s/trial/%s' % (API_ADDRESS, trial_id)
logging.info('PATCH %s' % url)
r = requests.patch(url, json=mm_trial, headers=headers)
r_code = r.status_code
if 199 < r_code < 300:
return json.dumps({"success": True})
else:
logging.error("error updating trial: %s" % protocol_no)
# return success
return json.dumps({"success": True})